AutismKB 2.0

Evidence Details for SHANK3


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Basic Information Top
Gene Symbol:SHANK3 ( DEL22q13.3,KIAA1650,PROSAP2,PSAP2,SPANK-2 )
Gene Full Name: SH3 and multiple ankyrin repeat domains 3
Band: 22q13.33
Quick LinksEntrez ID:85358; OMIM: 606230; Uniprot ID:F2Z3L0_HUMAN; ENSEMBL ID: ENSG00000251322; HGNC ID: 14294
Relate to Another Database: SFARIGene; denovo-db
Sequences Top
>SHANK3|85358|nucleotide
ATGGACGGCCCCGGGGCCAGCGCCGTGGTCGTGCGCGTCGGCATCCCGGACCTGCAGCAGACGAAGTGCCTGCGCCTGGACCCGGCCGCGCCCGTGTGGGCCGCC
AAGCAGCGCGTGCTCTGCGCCCTCAACCACAGCCTCCAGGACGCGCTCAACTATGGGCTTTTCCAGCCGCCCTCCCGGGGCCGCGCCGGCAAGTTCCTGGATGAG
GAGCGGCTCCTGCAGGAGTACCCGCCCAACCTGGACACGCCCCTGCCCTACCTGGAGTTTCGATACAAGCGGCGAGTTTATGCCCAGAACCTCATCGATGATAAG
CAGTTTGCAAAGCTTCACACAAAGGCGAACCTGAAGAAGTTCATGGACTACGTCCAGCTGCATAGCACGGACAAGGTGGCACGCCTGTTGGACAAGGGGCTGGAC
CCCAACTTCCATGACCCTGACTCAGGAGAGTGCCCCCTGAGCCTCGCAGCCCAGCTGGACAACGCCACGGACCTGCTAAAGGTGCTGAAGAATGGTGGTGCCCAC
CTGGACTTCCGCACTCGCGATGGGCTCACTGCCGTGCACTGTGCCACACGCCAGCGGAATGCGGCAGCACTGACGACCCTGCTGGACCTGGGGGCTTCACCTGAC
TACAAGGACAGCCGCGGCTTGACACCCCTCTACCACAGCGCCCTGGGGGGTGGGGATGCCCTCTGCTGTGAGCTGCTTCTCCACGACCACGCTCAGCTGGGGATC
ACCGACGAGAATGGCTGGCAGGAGATCCACCAGGCCTGCCGCTTTGGGCACGTGCAGCATCTGGAGCACCTGCTGTTCTATGGGGCAGACATGGGGGCCCAGAAC
GCCTCGGGGAACACAGCCCTGCACATCTGTGCCCTCTACAACCAGGAGAGCTGTGCTCGTGTCCTGCTCTTCCGTGGAGCTAACAGGGATGTCCGCAACTACAAC
AGCCAGACAGCCTTCCAGGTGGCCATCATCGCAGGGAACTTTGAGCTTGCAGAGGTTATCAAGACCCACAAAGACTCGGATGTTGTACCATTCAGGGAAACCCCC
AGCTATGCGAAGCGGCGGCGACTGGCTGGCCCCAGTGGCTTGGCATCCCCTCGGCCTCTGCAGCGCTCAGCCAGCGATATCAACCTGAAGGGGGAGGCACAGCCA
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>SHANK3|85358|protein
MDGPGASAVVVRVGIPDLQQTKCLRLDPAAPVWAAKQRVLCALNHSLQDALNYGLFQPPSRGRAGKFLDEERLLQEYPPNLDTPLPYLEFRYKRRVYAQNLIDDK
QFAKLHTKANLKKFMDYVQLHSTDKVARLLDKGLDPNFHDPDSGECPLSLAAQLDNATDLLKVLKNGGAHLDFRTRDGLTAVHCATRQRNAAALTTLLDLGASPD
YKDSRGLTPLYHSALGGGDALCCELLLHDHAQLGITDENGWQEIHQACRFGHVQHLEHLLFYGADMGAQNASGNTALHICALYNQESCARVLLFRGANRDVRNYN
SQTAFQVAIIAGNFELAEVIKTHKDSDVVPFRETPSYAKRRRLAGPSGLASPRPLQRSASDINLKGEAQPAASPGPSLRSLPHQLLLQRLQEEKDRDRDADQESN
ISGPLAGRAGQSKISDPGPGPGGVGGAPLPPPGAPRSCIRIRARFPAPPAPPAPPPRGPKRKLYSAVPGRKFIAVKAHSPQGEGEIPLHRGEAVKVLSIGEGGFW
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Evidence summary Top

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Evidences Syndromic Gene GWAS CNV Linkage Association Expression NGS de novo NGS Mosaic NGS Other Low-Scale Gene Studies Total
Score (No. of Studies) Yes 1 (1) 2 (14) 0 (0) 2 (4) 0 (0) 2 (7) 0 (0) 0 (0) 3 (5) 62 (31)
Syndromic Autism Gene Top
Abbreviations: AD, autosomal dominant; AR, autosomal recessive; ASD, autism spectrum disorder; ID, intellectual disability; XL, X linked.
InheritanceAD
OMIMChromosome 22q13.3 deletion syndrome (606232)
Description22q13 deletion syndrome (Phelan-McDermid syndrome) is caused by deletions of SHANK3; ASD or autistic features are frequent. SHANK3 mutations have also been reported in individuals with ASD
Reference(s)20186804; 17173049; 18615476; 19736351; 15286229; 17999366; 10735630;
LevelLevel 3: The gene has been reported in more than one family with ASD/autistic features, but the disorder hasn't been a generally acknowledged ASD related disorder.
Genome-Wide Association Studies (By Ethnic Group) Top
Family Based Association Studies: 1
Reference Stage Platform #Families Affecteds Result
#Subjects
(% Women)
ADI-R ADOS Diagnosis Age
(range)
IQ
(range)
MIXED/OTHERS
Connolly S, 2017_2 - Illumina 1Mv1;Illumina 1Mv3 Duo; Illumina HumanOmni2.5 M 2591 -
(-)
ASD -
-
-
-
Case Control Based Association Studies: 0
Reference Stage Platform ASD Cases Normal Controls Result
#Subjects
(% Women)
ADI-R ADOS Diagnosis Age
(range)
IQ #Subjects
(% Women)
Age
(range)
No Evidence.
CNV Studies Top
Reference Source Method ADI-R ADOS Diagnosis Family Individual
Total Simplex Multiplex Control Affected Control Total
Goizet, 2000 - FISHautism - - - - 1 - 1
Prasad, 2000 - FISHautism - - - - 1 - 1
Wassink, 2001 USA Chromosomal analysis of G-bandautism - - - - 278 - 278
Sebat, 2007 USA aCGHautism 165 118 47 99 195 196 391
Marshall, 2008 - SNP microarrayASD 427 238 189 - 427 500 927
Zwaag, 2009 - SNP microarrayautism - - - - 105 267 372
Pinto, 2010 - SNP microarray, qPCRASD - - - - 996 1287 2283
Chen, 2011 - FISH, aCGH--autism - - - - 1 - 1
Bremer, 2011 - aCGHASD - - - - 223 - 223
Sanders, 2011 Simons Simplex Collection SNP microarray--ASD 1127 1127 - - - - -
Sanders SJ, 2015 - ---ASD 2591 - - - - - -
Eriksson MA, 2015 Sweden FISH?--autism - - - - 162 - 162
Brownstein CA, 2016 - chromosomal microarray analysisautism - - - - 1 - 1
C Yuen RK, 2017 - WGSASD - - - - 1745 - -
Linkage Studies Top
Low Scale Association Studies (by Ethnic Group) Top
Family Based Association Studies: 2
Case Control Based Association Studies: 2
Reference Source Platfrom ASD Cases Normal Controls Result
ADI-R ADOS Diagnosis Age
(range)
IQ #Subjects
(% Women)
Age
(range)
CAUCASIAN
Koberstein JN, 2018_1 Unknown Life Technologies--ASD -
3.3 to 15.2 years
- 214
(-)
-
3.2 to 16.3 years
-
MIXED/OTHERS
Shao S, 2014_1 China PCRASD 4.63
-
- 636
(12.26%)
61.18
-
Qiu S, 2018_1 China PCR- -
-
- 241
(19.09%)
-
-
Large Scale Expression Studies Top
NGS de novo Mutation Studies Top
Reference Case Number Family Number de novo Number Title
De Rubeis S, 2014 2270 - 1702 Synaptic, transcriptional and chromatin genes disrupted in autism
O'Roak BJ, 2014 3486 - 59 Recurrent de novo mutations implicate novel genes underlying simplex autism risk.
Yuen RK, 2016 200 - 301 Genome-wide characteristics of de novo mutations in autism.
C Yuen RK, 2017 1625 - 237 Whole genome sequencing resource identifies 18 new candidate genes for autism spectrum disorder.
Zhu W, 2018 1 - 2 Two de novo novel mutations in one SHANK3 allele in a patient with autism and moderate intellectual
NGS Mosaic SNV Studies Top
NGS Other Studies Top
Low Scale Gene Studies Top

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Syndromic Genes

Non-syndromic Genes

AutismKB Statistics

  • Studies: 1,036
  • Genes: 1,379
  • CNVs/SVs: 5,420
  • SNVs/Indels: 11,669
  • de novo Mutations: 5,669
  • Mosaics: 789
  • Linkage Regions: 172
  • Paper Collected: 6/30/2018
  • Last Update: 8/26/2018